readSingleCellExperiment {scp} | R Documentation

## Read SingleCellExperiment from tabular data

### Description

Convert tabular data from a spreadsheet or a `data.frame` into a `SingleCellExperiment` object.

### Usage

    readSingleCellExperiment(table, ecol, fnames, ...)

### Arguments

`table` | File or object holding the quantitative data. Can be either a `character(1)` with the path to a text-based spreadsheet (comma-separated values by default, but see `...`) or an object that can be coerced to a `data.frame`. It is advised not to encode characters as factors.
`ecol` | A `numeric` indicating the indices of the columns to be used as assay values. Can also be a `character` indicating the names of the columns. Caution must be taken if the column names are composed of special characters like `(` or `-` that will be converted to a `.` by the `read.csv` function. If `ecol` does not match, the error message will dislpay the column names as seen by the `read.csv` function.
`fnames` | An optional `character(1)` or `numeric(1)` indicating the column to be used as row names.
`...` | Further arguments that can be passed on to read.csv except `stringsAsFactors`, which is always `FALSE`.

### Value

An instance of class SingleCellExperiment.

### Note

The `SingleCellExperiment` class is built on top of the `RangedSummarizedExperiment` class. This means that some column names are forbidden in the `rowData`. Avoid using the following names: `seqnames`, `ranges`, `strand`, `start`, `end`, `width`, `element`

### Author(s)

Laurent Gatto, Christophe Vanderaa

### See Also

The code relies on QFeatures::readSummarizedExperiment.

### Examples

    ## Load a data.frame with PSM-level data
    data("mqScpData")

    ## Create the QFeatures object
    sce <- readSingleCellExperiment(mqScpData,
                                    grep("RI", colnames(mqScpData)))

[Package scp version 1.4.0 Index]